Feature Article: Micro-Ecosystems

Imagine a device that has a water pump that sends water to the top of a tower and then releases it. As the water spills down due to force of gravity, the water spins a generator that in turn produces electrical energy to drive the pump, which sends more water to the top of the tower – and so on forever. As a youngster, I imagined such a perpetual motion device might work until my father (an electrical engineer) explained to me that friction, increasing entropy and the realities of conservation of energy would all combine to make such a device unworkable (on Earth at least).


Commercially available hermetically sealed micro-ecosystem.

Over the years, a similar idea has cropped up in aquarium keeping. Imagine being able to hold a sealed ecosystem in your hand, or have a totally closed micro-aquarium sitting on a shelf. The autotrophic algae and plants it contains would serve as food for the heterotrophic animals with the waste products from the animals serving as nutrients for the autotrophs. So, the animals in such a system would utilize the oxygen given off by photosynthetic organisms and they would in turn make use of the carbon dioxide and waste products given off by the animals to fuel their own growth. The only external energy input to such a system would be light. People have long sought to develop biological systems that would run forever like a perpetual motion device. The same sort of restrictions on perpetual motion devices will however, causes these closed ecosystems to wind down and eventually fail. Still, some aquarists are drawn to the idea of closed ecosystems, and by following some basic ideas, intriguing systems can be established and studied.

These ecosystems can either be “closed” or “open” in respect to energy. A completely closed system that does not have any energy input (even from light) is theoretically possible using chemotrophic bacteria. These systems would have little interest to aquarium hobbyists because they would need to be kept in the dark and the only organisms in them would be microscopic bacteria. Open systems (in respect to energy) allow for more interesting animals and plants to be maintained.


In attempting to define these ecosystems, it is helpful to consider the following variations on the theme. These four basic systems differ in the degree to which they are closed to the outside environment.

  1. Hermetically sealed micro-ecosystems: These systems are totally sealed in respect to any physical input from the environment around them. The primary energy input is the light that reaches the plants inside. Whatever air, water, nutrients and animals that are present when the ecosystem was sealed are all that are available to maintain the ecosystem.
  2. Closed systems: These ecosystems are closed to the environment around them with the exception that they allow for the passive exchange of atmospheric gasses. Again, the primary energy input is light to drive the process of photosynthesis. Most hermetically sealed ecosystems do not incorporate a sufficient amount of air in the system. By allowing exchanges of gases, these systems avoid that problem, but are still closed in respect to food energy, water changes and additions of plants or animals.
  3. Semi-closed systems: As with the closed systems described above, some gas exchange is allowed. In addition, the next most easily degraded component of these ecosystems – water quality, is kept within appropriate parameters by performing partial water changes. These water changes replace inorganic nutrients that may have become chemically or biologically bonded and thus removed from the ecosystem. Still, there is no energy added to the system except for light and sufficient heat to maintain a level proper for the organisms being maintained.
  4. Open systems: These systems rely on atmospheric gas and water exchanges as do semi-closed systems, but in addition, there are moderate inputs of supplemental food energy for the heterotrophic animals. This allows for a higher density of these organisms to be maintained – making a more aesthetically pleasing system. The only difference between open systems and a regular aquarium is that no active filtration is used, and the species present in the system are left unchanged, no new plants or animals are added.

A second energy pathway that needs to be considered in all four of these models is heat energy, or infrared radiation. Infrared radiation entering the system can have a profound affect on the plants and animals. Too low heat energy and some biological functions will shut down. Too much infrared radiation will cause the water temperature may rise to levels lethal to the plants and animals.

Anyone interested in experimenting with closed ecosystem aquariums, needs to have a reasonable expectations as to the results that will be obtained. Vertebrates, (fish in this case) are not well suited for living in micro-ecosystems; they should only be kept in properly maintained aquariums. This leaves invertebrates, algae and plants as suitable organisms for stocking the ecosystem. The hardier the species, the better, as these ecosystems sometimes experience wide fluctuations in their environmental conditions that may harm more delicate animals and plants. Micro-ecosystems also require a very low density of animals and plants. This helps keep the system more stable. Remember that most of the species suitable for these systems are not very large and are often not very colorful. If your desire is to have an ecosystem filled with all manner of organisms, your best bet would be to consider a regular aquarium. If on the other hand, the idea of a closed, or partially closed
ecosystem intrigues you, consider setting up a small system as described below.

The first step to take should you decide to try to build an ecosystem is to determine if you want to create a freshwater or marine habitat. It is advisable for beginning aquarists to choose a freshwater ecosystem, as their marine counterparts are more complicated to operate and seem to be inherently less stable. After the basic water type has been selected, decide which of the four types of ecosystems you wish to establish. After that, read the following section that describes that system and then determine what type of vessel you plan to use. Use your imagination in selecting a container to hold your ecosystem – antique bottles and vases have been used, as have five-gallon water carboys. Depending on the type of system, the top can either be left off or sealed with some temporary material such as wax.

Once the basic format of the ecosystem has been determined, choose appropriate species to add to the system, and follow the instructions in each section in terms of the order in which to add the specimens, as well as the amount of them to add. Table 1 lists some species that have been used to populate ecosystem aquariums.

Common NameScientific nameWater typeNotes
Willow mossFontinalis sp.FreshwaterPrefers cooler temperatures
Unequal arm starfishAsterina sp.MarineMay reproduce in captivity
Thallose algaeCaulerpa sp.MarineVery hardy, many species
ShrimpMysis sp.MarineUsually will not reproduce
Pond weedAnacharis / Elodea sp.FreshwaterHardy – lower light need
Malaysian snailMelanoides sp.FreshwaterHardy algae feeder
HornwortCeratophyllum sp.FreshwaterVery hardy – moderate light
Hermit crabPagurus sp.MarineUsually requires feeding
Glass anemoneAiptasia sp.MarineMay become a pest species
Chain algaeHalimeda sp.MarineRequires high calcium levels
Bubble algaeValonia sp.MarineMay become a pest
BladderwortUltricularia sp.FreshwaterDelicate
Table 1. Potential hardy species for ecosystem aquariums


Hermetically sealed ecosystems

This type of mini-ecosystem is considered the epitome of the genre; a totally enclosed system that only uses light energy to maintain the life functions of the animals and plants that reside, all locked inside. As mentioned, a truly self-sustaining, stable sealed ecosystem is really a pipe dream, no more achievable than a perpetual motion device. However, for the short term (months to perhaps a few years) these sealed systems may maintain stability. While they are in their prime condition, they are truly remarkable to observe. These systems are less decorative than the other systems because the animal and plant life they contain must be very small in order to survive and reproduce in such a small volume of water. The majority of the systems seen are sold as complete units called Ecospheres by a company that developed a system that incorporates a tiny red shrimp (Halocaridina rubra) and some algae. These ready-made units are rather expensive, but very


A hermetically sealed Ecosphere that is still viable after almost five years.


It is difficult to duplicate this sort of sealed ecosystem in the home. However, those who wish to try should begin with using some sand or gravel substrate from an existing aquarium. This allows for a mature population of microscopic plants and animals to already be present in the system prior to its being sealed. Since you only have one chance (when you first set the system up), balancing the energy cycle shown in figure one is impossible to do accurately, so just make your best guess. The system will reach equilibrium on its own as time goes on. Remember that most of these sealed ecosystems suffer from too high of a stocking density, so start with just a few specimens. Never try to incorporate a fish into a sealed system, this is cruel and the fish will soon die. For freshwater systems, consider using a few pond snails and a sprig of Hornwort or Anacharis plants. Marine systems can use Aiptasia sea anemones, Asterina starfish and Caulerpa algae.

Once the system has been sealed, the only variables that can be controlled by the aquarist are light and temperature. It is best to just keep the temperature stable, and concentrate on varying the light intensity in order to try to balance the system. If the algae or plants in the system seem to be fading or dying back, increase the light intensity and duration. If the plant life threatens to overwhelm the system, reduce the light by some amount.


Figure 1. Hermetically sealed ecosystem

It seems that at least some of these sealed systems do better if held under 24-hour lighting. While the plants are actively photosynthesizing, they absorb carbon dioxide and release oxygen. This causes the pH of the water to rise. At night, reverse phase photosynthesis occurs, and carbon dioxide is given off by both the plants and the animals. This can cause the pH to drop – possibly to a level that would prove fatal to the animals. By lighting the system with a moderate amount of light at all times, this radical swing in pH can be avoided. Of course, there is a tendency for the plants to overgrow the system when held under constant light, but this problem can be partially solved by increasing the distance between the ecosystem and its light source. Figure one diagrams a hermetically sealed aquarium system.

In one experiment, a five-gallon carboy was left sealed for ten years. Initially it was stocked with seawater and tiny pieces of live rock from an established aquarium. For the first year or so, some activity was seen inside – with populations of invertebrates and algae growing and changing. After that point, the system seemed to shut down with only a light coating of green algae evident – an interesting experiment, but not very attractive.


Five gallon carboy after being sealed for ten years.

In a previous life, this carboy had been used as a sealed terrarium with various houseplants. First pea gravel was added to the bottom of the empty carboy, followed by soil mixed with sphagnum moss. Plants were added by means of a long pair of forceps. The plastic cap was finally fitted in place. This terrarium suffered from algae growth on the inside glass of the carboy that could have been removed with either a cloth pad held in a pair of forceps, or possibly with a small aquarium cleaning magnet set. Pruning of the plants proved problematic with certain species overgrowing the others, and dead leaves building up on the surface of the soil.



Closed systems

Figure two illustrates a closed aquarium system. These differ from a sealed system in that they have some gas exchange with the air in the room in which they are housed. This helps reduce the severe pH shifts previously mentioned. In addition, some of the waste products from the animals are turned into nitrogen gas, which is then allowed to leave the system. Likewise, if the plants require more carbon dioxide than the system can provide for them, more of this gas can be taken from the room air. In all, these systems tend to be just a bit more forgiving than a completely sealed system. Like those, however, the only energy input is light, so that is the only controllable variable. In theory, the ambient temperature of the system could be changed to further control the system; raising the temperature will increase the rate of photosynthesis, while lowering the temperature will reduce the activity of both the plants and animals. The danger here is that the temperature change may end up being outside the range considered normal for the plants and animals that inhabit the system and the whole ecosystem might shut down. Many of the organisms used in these systems are tropical, stenothermic creatures – meaning that they require warm, stable temperatures in which to thrive.


Figure 2. Closed ecosystem.







Gas exchange is managed in this small closed system by periodically removing the lid.











Semi-closed systems


Figure 3. Semi-closed ecosystem.

Because waste products tend to build up in water while certain inorganic trace elements are depleted, all closed systems tend to wind down over time. By exchanging some of the water, wastes are removed from the system, while inorganic trace elements are replenished. Figure three illustrates a semi-closed system. The only energy source remains light energy, but now waste products produced by bacteria can be removed and inorganic nutrients (trace elements) are added. The amount of water changes required for these systems varies, and there is no hard and fast rule, but consider performing a 50% water change each month as a starting point. If the plants and animals go into a decline, increase the amount or frequency of the water changes to try to correct the problem.


Open systems


Water changes are easily performed on this six-ounce semi-closed ecosystem.

Finally, figure four illustrates an open ecosystem. These systems have the most liberal requirements of all the closed ecosystems discussed in this article. They are really just aquariums that do not have an active filtration system – relying instead on passive nitrification to detoxify waste products produced by the animals. This is the only ecosystem that you should ever consider adding fish to – and then, only if the system is large enough.

One example of an open system was named FIB by its creator, a public aquarium curator. FIB stands for “Fish In a Bottle”. This experiment was a goldfish that lived for over nine years in a glass carboy. No filtration was used, just an open air stem bubbling for aeration. Water quality was maintained through passive nitrification from the bacteria living on the surface of the gravel, as well as frequent and generous water changes. The inside of the glass was cleaned using a scrubbing pad gripped in a pair of tongs. The fish was fed a wide variety of foods including earthworms, mealworms, trout chow and flake foods. Over the years FIB grew to the point that it would no longer fit through the neck of the bottle! FIB was developed as a demonstration of how fish can thrive in small containers when given excellent care, but it was also a very good example of an open ecosystem.

Another commonly cited example of an open system were the “natural” aquariums promoted by the late Lee Chin Eng while living in Indonesia in the 1960’s. He was reportedly able to keep all manner of fish, corals and other invertebrates in marine aquariums with no filtration, just a slow trickle of air. We really only have his photographs to document these systems, however quite a bit can be deduced from them by careful observation: Some of the photos show shrimpfish being kept alongside damselfish, clownfish and batfish. Anyone who has successfully kept shrimpfish knows that they do best if fed live mysid shrimp, and cannot compete with those other species of fish for food. Therefore, it seems that Mr. Eng added these shrimpfish a short time before taking the photo – and may have done the same with some of the more delicate invertebrates in his demonstration tanks. Other images of his systems show corals placed in unnatural positions, showing no evidence of any in-situ growth.


Figure 4. Open ecosystem

Many of the other organisms seen are hardy species (at least for the short term) such as feather dusters, carpet anemones and red Fromia sp. starfish. Mr. Eng evidently established basic marine aquariums with live rock and sturdy animals, and then just prior to being photographed, he “spruced the tanks up” by adding a few showy, but more delicate species. No magic here, just easy access to clean seawater, live rock, tropical sunlight and lots of cool animals to replace any that died.


Maintenance tips

Since the goal of these systems is self-sufficiency, once they are operating, there is the intent that there should be little intervention required by the aquarist. One exception to this idea is that of pest algae removal.


Six ounce semi-closed ecosystem after one month.

There is a constant struggle in all of these systems for one species of life to gain the upper hand, and one technique used to accomplish this is for algae to grow on the inside surface of the container, effectively stealing the light away from any photosynthetic organisms living inside the container itself. Scientists call this “self-shading” and it occurs in natural systems as well, where free-floating algae grows at the surface, hijacking any light from reaching further down in the water column. In a controlled ecosystem, this means that unless controlled, the ecosystem may end up consisting of a thick coating of algae on the inside surface of the container, and little else. Using biological controls doesn’t work well in that adding extra numbers of these species would tend to unbalance the system. For open systems, it is always best to control slime algae by physically removing it with a bit of scrubber pad held with a pair of tongs.

All of these systems will require a great degree of experimentation on the part of the aquarist in order for them to run correctly. Since many aquarists love to tinker and work on “Do It Yourself” projects, this is never a major obstacle. It does however, help to have larger, properly operating aquariums in which to grow various plants and animals that you intend to try out in your ecosystems. That way, if one species doesn’t do well, you can replace it with another and try it out instead.


Six ounce semi-closed ecosystem after one year with no maintenance.

If this topic intrigues you and you eventually decide to try one of these systems, remember to always be sensitive to the husbandry requirements of any animals you intend to add to the system. Don’t “push the envelope” by trying to maintain higher animals such as fish in very small closed systems, or overcrowding them, or in other ways risking their lives. Always treat your animals with respect, empathy and the best possible care you that you can.

One final piece of advice that may be contrary to what seems to be common sense; start small; larger closed -eco-systems are not inherently more stable (as evidenced by the largest closed ecosystem of all – the Earth). The balance of our Earth is so fragile that humans have caused major disruptions such as global warming, pollution and extinction of species in a very short time. It is presumptuous for any of us then to assume that we can build a large sealed ecosystem that would be stable enough to last for months or even years.

When experimenting with these small scale closed systems, it is vitally important to be backed up by your already solidly operating typical marine aquariums, so that you are better prepared to ultimately succeed with these experimental closed mini eco-systems.



  1. Hemdal, J.F. 2008. Miniature Aquariums (In Press). 144pp. BowTie Press, Irvine, California
  2. Hemdal, J.F. 2006. Advanced Marine Aquarium Techniques. 352pp. TFH publications, neptune City, New Jersey
  3. Hemdal, J.F. 1984. A Miniature Ocean. SeaScope 1:1.
  4. Hemdal, J.F. 1981. Energy in the Marine Aquarium. Freshwater and Marine Aquarium 4(11):20.
  Advanced Aquarist, Advanced Aquarist

 Jay Hemdal

  (15 articles)

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